--- a/C and D finder/CandD.R	Wed Dec 11 13:35:46 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1122 +0,0 @@
-FirstSubstrateSet<- read.csv("input1.csv", stringsAsFactors=FALSE, header = FALSE)
-Firstsubbackfreq<- read.csv("input2.csv", header=FALSE, stringsAsFactors=FALSE)
-FirstSubstrateSet<- FirstSubstrateSet[2:nrow(FirstSubstrateSet),]
-
-SecondSubstrateSet<- read.csv("input3.csv", stringsAsFactors=FALSE, header = FALSE)
-Secondsubbackfreq<- read.csv("input4.csv", header=FALSE, stringsAsFactors=FALSE)
-SecondSubstrateSet<- SecondSubstrateSet[2:nrow(SecondSubstrateSet),]
-
-
-ThirdSubstrateSet<- read.csv("input5.csv", stringsAsFactors=FALSE, header = FALSE)
-Thirdsubbackfreq<- read.csv("input6.csv", header=FALSE, stringsAsFactors=FALSE)
-ThirdSubstrateSet<- ThirdSubstrateSet[2:nrow(ThirdSubstrateSet),]
-
-
-args = commandArgs(trailingOnly=TRUE)
-
-print(args[1])
-print(args[2])
-print(args[3])
-
-
-#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
-FullMotifsOnly_questionmark<-args[1]
-#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
-TruncatedMotifsOnly_questionmark<-args[2]
-#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps)
-Are_You_Looking_For_Commonality<-args[3]
-
-
-#then put the names of your output files here
-Shared_motifs_table<-"sharedmotifs.csv"
-Shared_subbackfreq_table<-"sharedSBF.csv"
-
-# Shared_motifs_table<-"Shared motifs 7-27-17.csv"
-# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"
-
-First_unshared_motifs_table<-"R1 substrates.csv"
-First_unshared_subbackfreq<-"R1 SBF.csv"
-
-Second_unshared_motifs_table<-"R2 subs.csv"
-Second_unshared_subbackfreq<-"R2 SBf.csv"
-
-Third_unshared_motifs_table<-"R3 subs.csv"
-Third_unshared_subbackfreq<-"R3 SBF.csv"
-
-#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles.  I think I'll poke around
-#other languages to see if any of them can do it.
-####################################################################################################################################
-
-
-
-
-
-FirstxY<-rep("xY",times=nrow(FirstSubstrateSet))
-FirstSubstrateSet[,11]<-FirstxY
-
-SecondxY<-rep("xY",times=nrow(SecondSubstrateSet))
-SecondSubstrateSet[,11]<-SecondxY
-
-ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet))
-ThirdSubstrateSet[,11]<-ThirdxY
-
-
-
-
-
-
-
-
-
-
-
-####################################################################################################################################
-####################################################################################################################################
-# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two 
-# separate proteins thus two separate accession numbers?
-# It should actually output the shared motif and BOTH accession numbers.  Right now it does not, it only maps out the second
-# accession number.  So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number
-####################################################################################################################################
-####################################################################################################################################
-####################################################################################################################################
-####################################################################################################################################
-
-#Create the motif sets, deciding wether or not you're looking for truncated or full here
-#full only
-if (Are_You_Looking_For_Commonality=="YES"){
-  if (FullMotifsOnly_questionmark=="YES"){
-    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    leftspaces<-c()
-    rightspaces<-c()
-    for (i in 1:nrow(FirstSubstrateSet)){
-      FTLwtletters<-FirstSubstrateSet[i,4:18]
-      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-      
-      
-      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
-        motif<-YYYmotif
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i,1]<-FTLwtletters
-        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-        
-      }
-      
-    }
-    # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
-    # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
-    # 
-    
-    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
-    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
-    
-    for (i in 1:nrow(SecondSubstrateSet)){
-      D835letters<-SecondSubstrateSet[i,4:18]
-      D835letters<-D835letters[D835letters !="XXXXX"]
-      D835letters<-paste(D835letters, sep="", collapse="")
-      
-      
-      YYYmotif <- unlist(strsplit(D835letters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
-        motif<-YYYmotif
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        D835letters<-motif
-        D835Ymotifs[i,1]<-D835letters
-        D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
-        
-      }
-    }
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    for (i in 1:nrow(ThirdSubstrateSet)){
-      ITDletters<-ThirdSubstrateSet[i,4:18]
-      ITDletters<-ITDletters[ITDletters !="XXXXX"]
-      ITDletters<-paste(ITDletters, sep="", collapse="")
-      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
-        motif<-YYYmotif
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        ITDletters<-motif
-        ITDmotifs[i,1]<-ITDletters
-        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
-        
-      }
-    }
-    
-  }
-  
-  ##############################################3
-  #Truncated only
-  if (TruncatedMotifsOnly_questionmark=="YES"){
-    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    
-    for (i in 1:nrow(FirstSubstrateSet)){
-      FTLwtletters<-FirstSubstrateSet[i,4:18]
-      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-      
-      
-      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i,1]<-FTLwtletters
-        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-      
-    }
-    
-    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
-    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
-    
-    for (i in 1:nrow(SecondSubstrateSet)){
-      D835letters<-SecondSubstrateSet[i,4:18]
-      D835letters<-D835letters[D835letters !="XXXXX"]
-      D835letters<-paste(D835letters, sep="", collapse="")
-      
-      
-      YYYmotif <- unlist(strsplit(D835letters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        D835letters<-motif
-        D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
-        D835Ymotifs[i,1]<-D835letters
-      }
-    }
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    for (i in 1:nrow(ThirdSubstrateSet)){
-      ITDletters<-ThirdSubstrateSet[i,4:18]
-      ITDletters<-ITDletters[ITDletters !="XXXXX"]
-      ITDletters<-paste(ITDletters, sep="", collapse="")
-      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        ITDletters<-motif
-        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
-        ITDmotifs[i,1]<-ITDletters
-      }
-    }
-    
-  }
-  
-  ###############################################
-  #ALL motifs, full and truncated
-  
-  if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
-    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    
-    for (i in 1:nrow(FirstSubstrateSet)){
-      FTLwtletters<-FirstSubstrateSet[i,4:18]
-      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-      leftspaces<-c()
-      rightspaces<-c()
-      
-      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i,1]<-FTLwtletters
-        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-      
-      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
-        motif<-YYYmotif
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i,1]<-FTLwtletters
-        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-        
-        
-      }
-      
-    }
-    
-    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
-    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
-    
-    for (i in 1:nrow(SecondSubstrateSet)){
-      D835letters<-SecondSubstrateSet[i,4:18]
-      D835letters<-D835letters[D835letters !="XXXXX"]
-      D835letters<-paste(D835letters, sep="", collapse="")
-      leftspaces<-c()
-      rightspaces<-c()
-      
-      YYYmotif <- unlist(strsplit(D835letters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        D835letters<-motif
-        D835Ymotifs[i,1]<-D835letters
-        D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-      
-      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
-        motif<-YYYmotif
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        D835letters<-motif
-        D835Ymotifs[i,1]<-D835letters
-        D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-    }
-    
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    for (i in 1:nrow(ThirdSubstrateSet)){
-      ITDletters<-ThirdSubstrateSet[i,4:18]
-      ITDletters<-ITDletters[ITDletters !="XXXXX"]
-      ITDletters<-paste(ITDletters, sep="", collapse="")
-      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
-      leftspaces<-c()
-      rightspaces<-c()
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        ITDletters<-motif
-        ITDmotifs[i,1]<-ITDletters
-        ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-      
-      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
-        motif<-YYYmotif
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        ITDletters<-motif
-        ITDmotifs[i,1]<-ITDletters
-        ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-    }
-    
-  }
-  #############################################################################################################################
-  #############################################################################################################################
-  #############################################################################################################################
-  #############################################################################################################################
-  #############################################################################################################################
-  
-  #now look for either commonality or difference.  Actually could you look for both...
-  
-  if (Are_You_Looking_For_Commonality=="YES"){
-    
-    columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
-    columnalheader<-matrix(columnalheader,nrow = 1)
-    # write.table(x=columnalheader,
-    #             file=Shared_subbackfreq_table,
-    #             quote=FALSE, sep=",",
-    #             row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-    
-    FirstOverlapmotifs<-c()
-    for (i in 1:nrow(ITDmotifs)){
-      for (j in 1:nrow(D835Ymotifs)){
-        if (is.na(ITDmotifs[i,1])!=TRUE&&is.na(D835Ymotifs[j,1])!=TRUE){
-          if (ITDmotifs[i,1]==D835Ymotifs[j,1]){
-            FirstOverlapmotifs<-c(FirstOverlapmotifs,D835Ymotifs[j,1])
-          }
-        }
-      }
-    }
-    
-    AllAccessionNumbers<-c()
-    columnalheader<-c(rep(NA,36))
-    FinalMatrix<-matrix(data =columnalheader,nrow = 1)
-    
-    FinalMotifs<-c(rep(NA,20))
-    FinalMotifsMatrix<-matrix(data = FinalMotifs,nrow = 1)
-    
-    
-    for (l in 1:length(FirstOverlapmotifs)) {
-      AccessionNumber<-00000000000
-      for (k in 1:nrow(FTLwtmotifs)) {
-        AccessionNumber<-0000000000000
-        if(is.na(FTLwtmotifs[k])!=TRUE){
-          #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
-          #destroyed immediately after use
-          if (FirstOverlapmotifs[l] == FTLwtmotifs[k]) {
-            substratematrix<-FirstSubstrateSet[k,1:20]
-            substratematrix<-as.matrix(substratematrix,nrow=1)
-            FinalMotifsMatrix<-rbind(FinalMotifsMatrix,substratematrix)
-            #when you find a match between the venn diagrams, save the substrate info you get into a matrix
-            
-            AccessionNumber <- as.character(FirstSubstrateSet[k, 3])
-            #then take the accession number 
-            
-            for (m in 1:ncol(Firstsubbackfreq)) {
-              AN <- as.character(Firstsubbackfreq[1, m])
-              if (grepl(pattern = AN,
-                        x = AccessionNumber,
-                        fixed = TRUE) == TRUE) {
-                outputmatrix <- as.character(Firstsubbackfreq[, m])
-                outputmatrix <- matrix(outputmatrix, nrow = 1)
-                #with that accession number, find a match in the subbackfreq file and save it here
-                FinalMatrix<-rbind(FinalMatrix,outputmatrix)
-              }
-            }
-          }
-        }
-      }
-    }
-    
-    
-    TrueMatrix<-FinalMatrix[!duplicated(FinalMatrix),]
-    TrueFinalMotifsMatrix<-FinalMotifsMatrix[!duplicated(FinalMotifsMatrix),]
-    
-    TrueFinalMotifsMatrix<-TrueFinalMotifsMatrix[2:nrow(TrueFinalMotifsMatrix),]
-    TrueMatrix<-TrueMatrix[2:nrow(TrueMatrix),]
-    
-    write.table(
-      x = TrueFinalMotifsMatrix,
-      file = Shared_motifs_table,
-      quote = FALSE,
-      sep = ",",
-      row.names = FALSE,
-      col.names = TRUE,
-      na = "",
-      append = FALSE
-    )
-    
-    #TrueMatrix<-t(TrueMatrix)
-    columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
-    columnalheader<-matrix(columnalheader,nrow = 1)
-    
-    TrueMatrix<-rbind(columnalheader,TrueMatrix)
-    TrueMatrix<-t(TrueMatrix)
-    
-    write.table(
-      x = TrueMatrix,
-      file = Shared_subbackfreq_table,
-      quote = FALSE,
-      sep = ",",
-      row.names = FALSE,
-      col.names = FALSE,
-      na = "",
-      append = TRUE
-    )
-  }
-}
-
-if (Are_You_Looking_For_Commonality=="NO"){
-  if (FullMotifsOnly_questionmark=="YES"){
-    FTLwtmotifs=rep(NA,times=nrow(FirstSubstrateSet))
-    FTLwtAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
-    leftspaces<-c()
-    rightspaces<-c()
-    for (i in 1:nrow(FirstSubstrateSet)){
-      FTLwtletters<-FirstSubstrateSet[i,4:18]
-      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-      
-      
-      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
-        motif<-YYYmotif
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i]<-FTLwtletters
-        FTLwtAccessionNumbers[i]<-FirstSubstrateSet[i,3]
-      }
-      
-    }
-    # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
-    # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
-    # 
-    
-    D835Ymotifs=rep(NA,times=nrow(FirstSubstrateSet))
-    D835YAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
-    
-    for (i in 1:nrow(SecondSubstrateSet)){
-      D835letters<-SecondSubstrateSet[i,4:18]
-      D835letters<-D835letters[D835letters !="XXXXX"]
-      D835letters<-paste(D835letters, sep="", collapse="")
-      
-      
-      YYYmotif <- unlist(strsplit(D835letters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
-        motif<-YYYmotif
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        D835letters<-motif
-        D835Ymotifs[i]<-D835letters
-        D835YAccessionNumbers[i]<-SecondSubstrateSet[i,3]
-      }
-    }
-    
-    ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet))
-    ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
-    
-    for (i in 1:nrow(ThirdSubstrateSet)){
-      ITDletters<-ThirdSubstrateSet[i,4:18]
-      ITDletters<-ITDletters[ITDletters !="XXXXX"]
-      ITDletters<-paste(ITDletters, sep="", collapse="")
-      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
-        motif<-YYYmotif
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        ITDletters<-motif
-        ITDmotifs[i]<-ITDletters
-        ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3]
-        
-      }
-    }
-    names(ITDmotifs)<-ITDAccessionNumbers
-    names(D835Ymotifs)<-D835YAccessionNumbers
-    names(FTLwtmotifs)<-FTLwtAccessionNumbers
-  }
-  
-  
-  ##############################################3
-  #Truncated only
-  if (TruncatedMotifsOnly_questionmark=="YES"){
-    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    
-    for (i in 1:nrow(FirstSubstrateSet)){
-      FTLwtletters<-FirstSubstrateSet[i,4:18]
-      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-      
-      
-      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i,1]<-FTLwtletters
-        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-      
-    }
-    
-    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
-    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
-    i=2
-    for (i in 1:nrow(SecondSubstrateSet)){
-      D835letters<-SecondSubstrateSet[i,4:18]
-      D835letters<-D835letters[D835letters !="XXXXX"]
-      D835letters<-paste(D835letters, sep="", collapse="")
-      
-      
-      YYYmotif <- unlist(strsplit(D835letters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        D835letters<-motif
-        D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
-        D835Ymotifs[i,1]<-D835letters
-      }
-    }
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    for (i in 1:nrow(ThirdSubstrateSet)){
-      ITDletters<-ThirdSubstrateSet[i,4:18]
-      ITDletters<-ITDletters[ITDletters !="XXXXX"]
-      ITDletters<-paste(ITDletters, sep="", collapse="")
-      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        ITDletters<-motif
-        ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
-        ITDmotifs[i,1]<-ITDletters
-      }
-    }
-    names(FTLwtmotifs)<-FTLwtAccessionNumbers
-    names(D835Ymotifs)<-D835YAccessionNumbers
-    names(ITDmotifs)<-ITDAccessionNumbers
-  }
-  
-  ###############################################
-  #ALL motifs, full and truncated
-  
-  if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
-    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
-    
-    for (i in 1:nrow(FirstSubstrateSet)){
-      FTLwtletters<-FirstSubstrateSet[i,4:18]
-      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
-      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
-      leftspaces<-c()
-      rightspaces<-c()
-      
-      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      
-      
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i,1]<-FTLwtletters
-        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-      
-      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
-        motif<-YYYmotif
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        FTLwtletters<-motif
-        FTLwtmotifs[i,1]<-FTLwtletters
-        FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-        
-        
-      }
-      
-    }
-    
-    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
-    D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
-    
-    for (i in 1:nrow(SecondSubstrateSet)){
-      D835letters<-SecondSubstrateSet[i,4:18]
-      D835letters<-D835letters[D835letters !="XXXXX"]
-      D835letters<-paste(D835letters, sep="", collapse="")
-      leftspaces<-c()
-      rightspaces<-c()
-      
-      YYYmotif <- unlist(strsplit(D835letters, split = ""))
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        D835letters<-motif
-        D835Ymotifs[i,1]<-D835letters
-        D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-      
-      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
-        motif<-YYYmotif
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        D835letters<-motif
-        D835Ymotifs[i,1]<-D835letters
-        D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-    }
-    
-    
-    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
-    ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
-    
-    for (i in 1:nrow(ThirdSubstrateSet)){
-      ITDletters<-ThirdSubstrateSet[i,4:18]
-      ITDletters<-ITDletters[ITDletters !="XXXXX"]
-      ITDletters<-paste(ITDletters, sep="", collapse="")
-      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
-      leftspaces<-c()
-      rightspaces<-c()
-      YYYposition <- match(x = "x", table = YYYmotif)
-      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
-      #just 3 letters to the left of x
-      
-      YYYLettersToTheLeft <- YYYposition - 1
-      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
-      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
-      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
-      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
-      #variable the user puts in is
-      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
-        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
-        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        ITDletters<-motif
-        ITDmotifs[i,1]<-ITDletters
-        ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-      
-      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
-        motif<-YYYmotif
-        #add blank spaces if the motif has less than 4 letters to the left/right
-        motif<-c(leftspaces,YYYmotif,rightspaces)
-        #save that motif, which is the Y and +/- 4 amino acids, including truncation
-        motif<-motif[!motif %in% "x"]
-        motif<-paste(motif, sep="", collapse="")
-        ITDletters<-motif
-        ITDmotifs[i,1]<-ITDletters
-        ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
-      }
-    }
-    names(FTLwtmotifs)<-FTLwtAccessionNumbers
-    names(D835Ymotifs)<-D835YAccessionNumbers
-    names(ITDmotifs)<-ITDAccessionNumbers
-  }
-  
-  
-  FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
-  FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs]
-  FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
-  
-  
-  ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs]
-  ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs]
-  ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)]
-  
-  
-  D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
-  D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs]
-  D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
-  
-  
-  columnalheader<-c(rep(NA,36))
-  FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-  
-  for (k in 1:length(FTLwtmotifsFINAL)) {
-    AN<-00000
-    #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
-    #destroyed immediately after use
-    for (m in 1:ncol(Firstsubbackfreq)) {
-      AN <- as.character(Firstsubbackfreq[1, m])
-      if (grepl(pattern = AN,
-                x = names(FTLwtmotifsFINAL[k]),
-                fixed = TRUE) == TRUE) {
-        outputmatrix <- as.character(Firstsubbackfreq[, m])
-        outputmatrix <- matrix(outputmatrix, nrow = 1)
-        #with that accession number, find a match in the subbackfreq file and save it here
-        FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
-      }
-    }
-  }
-  FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),]
-  
-  columnalheader<-c(rep(NA,36))
-  ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-  
-  for (k in 1:length(ITDmotifsFINAL)) {
-    AN<-00000
-    #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
-    #destroyed immediately after use
-    for (m in 1:ncol(Thirdsubbackfreq)) {
-      AN <- as.character(Thirdsubbackfreq[1, m])
-      if (grepl(pattern = AN,
-                x = names(ITDmotifsFINAL[k]),
-                fixed = TRUE) == TRUE) {
-        outputmatrix <- as.character(Thirdsubbackfreq[, m])
-        outputmatrix <- matrix(outputmatrix, nrow = 1)
-        #with that accession number, find a match in the subbackfreq file and save it here
-        ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix)
-      }
-    }
-  }
-  ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),]
-  
-  columnalheader<-c(rep(NA,36))
-  D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
-  
-  for (k in 1:length(D835YmotifsFINAL)) {
-    #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
-    #destroyed immediately after use
-    for (m in 1:ncol(Secondsubbackfreq)) {
-      AN <- as.character(Secondsubbackfreq[1, m])
-      if (grepl(pattern = AN,
-                x = names(D835YmotifsFINAL[k]),
-                fixed = TRUE) == TRUE) {
-        outputmatrix <- as.character(Secondsubbackfreq[, m])
-        outputmatrix <- matrix(outputmatrix, nrow = 1)
-        #with that accession number, find a match in the subbackfreq file and save it here
-        D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix)
-      }
-    }
-  }
-  D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),]
-  
-  FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2)
-  
-  #another fucking for loop
-  FLTreference<-FTLoutputmatrix[,2]
-  
-  FirstLine<-colnames(FirstSubstrateSet)
-  FirstLine<-FirstLine[1:23]
-  for (q in 1:nrow(FTLoutputmatrix)) {
-    thismotif<-unlist(strsplit(FTLoutputmatrix[q,1],""))
-    thisoutput<-c("","",FTLoutputmatrix[q,2],thismotif,"","","","","")
-    FirstLine<-rbind(FirstLine,thisoutput)
-  }
-  
-  
-  
-  write.table(x=FirstLine,
-              file=First_unshared_motifs_table,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-  columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
-  columnalheader<-matrix(columnalheader,nrow = 1)
-  
-  # columnalheader<-rbind(columnalheader,FTLFinalMatrix)
-  
-  write.table(x=columnalheader,
-              file=First_unshared_subbackfreq,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-  write.table(x=FTLFinalMatrix[2:nrow(FTLFinalMatrix),],
-              file=First_unshared_subbackfreq,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-  ############################################################################################################
-  
-  D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2)
-
-  FLTreference<-D835Youtputmatrix[,2]
-  
-  FirstLine<-colnames(FirstSubstrateSet)
-  FirstLine<-FirstLine[1:23]
-  for (q in 1:nrow(D835Youtputmatrix)) {
-    thismotif<-unlist(strsplit(D835Youtputmatrix[q,1],""))
-    thisoutput<-c("","",D835Youtputmatrix[q,2],thismotif,"","","","","")
-    FirstLine<-rbind(FirstLine,thisoutput)
-  }
-  
-  
-    
-  write.table(x=FirstLine,
-              file=Second_unshared_motifs_table,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-  columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
-  columnalheader<-matrix(columnalheader,nrow = 1)
-  
-  # columnalheader<-rbind(columnalheader,D835YFinalMatrix)
-  
-  write.table(x=columnalheader,
-              file=Second_unshared_subbackfreq,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-  write.table(x=D835YFinalMatrix[2:nrow(D835YFinalMatrix),],
-              file=Second_unshared_subbackfreq,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-  ############################################################################################################
-  
-  ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2)
-  
-  FLTreference<-ITDoutputmatrix[,2]
-  
-  FirstLine<-colnames(FirstSubstrateSet)
-  FirstLine<-FirstLine[1:23]
-  for (q in 1:nrow(ITDoutputmatrix)) {
-    thismotif<-unlist(strsplit(ITDoutputmatrix[q,1],""))
-    thisoutput<-c("","",ITDoutputmatrix[q,2],thismotif,"","","","","")
-    FirstLine<-rbind(FirstLine,thisoutput)
-  }
-  
-  
-  write.table(x=FirstLine,
-              file=Third_unshared_motifs_table,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-  columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
-  columnalheader<-matrix(columnalheader,nrow = 1)
-  
-  # columnalheader<-rbind(columnalheader,ITDFinalMatrix)
-
-  write.table(x=columnalheader,
-              file=Third_unshared_subbackfreq,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-  write.table(x=ITDFinalMatrix[2:nrow(ITDFinalMatrix),],
-              file=Third_unshared_subbackfreq,
-              quote=FALSE, sep=",",
-              row.names=FALSE,col.names = FALSE, na="", append=TRUE)
-  
-}

--- a/C and D finder/CandD.xml	Wed Dec 11 13:35:46 2019 -0500
+++ b/C and D finder/CandD.xml	Fri Feb 21 16:38:55 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="commonality_r" name="commonality_finder" version="1.0.0">
+<tool id="commonality_r" name="commonality_finder" version="1.1.0">
     <description>finds commonality</description>
     <requirements>
        <requirement type="package">R</requirement>
@@ -11,7 +11,7 @@
 		ln -s '$input5' input5.csv &&
 		ln -s '$input6' input6.csv &&
 		
-		Rscript '$__tool_directory__/CandD.R' NO NO YES
+		Rscript '$__tool_directory__/commonality-working feb 21 20.R'
     ]]></command>
     <inputs>
 		<param format="csv" name="input1" type="data" label="First Substrate Set"/>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/C and D finder/commonality-working feb 21 20.R	Fri Feb 21 16:38:55 2020 -0500
@@ -0,0 +1,302 @@
+FirstSubstrateSet<- read.csv("r1sub.csv", stringsAsFactors=FALSE, header = FALSE)
+Firstsubbackfreq<- read.csv("r1sbf.csv", header=FALSE, stringsAsFactors=FALSE)
+SubstrateHeader<-FirstSubstrateSet[1,]
+FirstSubstrateSet<- FirstSubstrateSet[2:nrow(FirstSubstrateSet),]
+if(nrow(Firstsubbackfreq[1,]>35)){
+  if(grepl(pattern = "Properties", x=Firstsubbackfreq[1,22])){
+    Firstsubbackfreq<-t(Firstsubbackfreq)
+  }
+}
+
+
+SecondSubstrateSet<- read.csv("r1sub.csv", stringsAsFactors=FALSE, header = FALSE)
+Secondsubbackfreq<- read.csv("r1sbf.csv", header=FALSE, stringsAsFactors=FALSE)
+SecondSubstrateSet<- SecondSubstrateSet[2:nrow(SecondSubstrateSet),]
+if(nrow(Secondsubbackfreq[1,]>35)){
+  if(grepl(pattern = "Properties", x=Secondsubbackfreq[1,22])){
+    Secondsubbackfreq<-t(Secondsubbackfreq)
+  }
+}
+
+
+ThirdSubstrateSet<- read.csv("r2sub.csv", stringsAsFactors=FALSE, header = FALSE)
+Thirdsubbackfreq<- read.csv("r2sbf.csv", header=FALSE, stringsAsFactors=FALSE)
+ThirdSubstrateSet<- ThirdSubstrateSet[2:nrow(ThirdSubstrateSet),]
+if(nrow(Thirdsubbackfreq[1,]>35)){
+  if(grepl(pattern = "Properties", x=Thirdsubbackfreq[1,22])){
+    Thirdsubbackfreq<-t(Thirdsubbackfreq)
+  }
+}
+
+
+
+
+#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
+FullMotifsOnly_questionmark<-"NO"
+#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
+TruncatedMotifsOnly_questionmark<-"NO"
+#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps)
+Are_You_Looking_For_Commonality<-"YES"
+
+
+#then put the names of your output files here
+Shared_motifs_table<-"sharedmotifs.csv"
+Shared_subbackfreq_table<-"sharedSBF.csv"
+
+# Shared_motifs_table<-"Shared motifs 7-27-17.csv"
+# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"
+
+First_unshared_motifs_table<-"R1 substrates.csv"
+First_unshared_subbackfreq<-"R1 SBF.csv"
+
+Second_unshared_motifs_table<-"R2 subs.csv"
+Second_unshared_subbackfreq<-"R2 SBf.csv"
+
+Third_unshared_motifs_table<-"R3 subs.csv"
+Third_unshared_subbackfreq<-"R3 SBF.csv"
+
+#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles.  I think I'll poke around
+#other languages to see if any of them can do it.
+####################################################################################################################################
+
+
+
+
+
+FirstxY<-rep("xY",times=nrow(FirstSubstrateSet))
+FirstSubstrateSet[,11]<-FirstxY
+
+SecondxY<-rep("xY",times=nrow(SecondSubstrateSet))
+SecondSubstrateSet[,11]<-SecondxY
+
+ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet))
+ThirdSubstrateSet[,11]<-ThirdxY
+
+
+
+
+
+
+
+
+
+
+
+####################################################################################################################################
+####################################################################################################################################
+# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two 
+# separate proteins thus two separate accession numbers?
+# It should actually output the shared motif and BOTH accession numbers.  Right now it does not, it only maps out the second
+# accession number.  So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number
+####################################################################################################################################
+####################################################################################################################################
+####################################################################################################################################
+####################################################################################################################################
+
+#Create the motif sets, deciding wether or not you're looking for truncated or full here
+#full only
+ 
+FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+FTLwtAccessionNumbers=matrix(data = Firstsubbackfreq[1,],ncol=1)
+
+for (i in 1:nrow(FirstSubstrateSet)){
+  FTLwtletters<-FirstSubstrateSet[i,4:18]
+  FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
+  FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
+  leftspaces<-c()
+  rightspaces<-c()
+  
+  YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
+  YYYposition <- match(x = "x", table = YYYmotif)
+  #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+  #just 3 letters to the left of x
+  
+  YYYLettersToTheLeft <- YYYposition - 1
+  #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+  #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+  YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+  #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+  #variable the user puts in is
+  
+  
+  if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+    leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+    rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+    #add blank spaces if the motif has less than 4 letters to the left/right
+    motif<-c(leftspaces,YYYmotif,rightspaces)
+    #save that motif, which is the Y and +/- 4 amino acids, including truncation
+    motif<-motif[!motif %in% "x"]
+    motif<-paste(motif, sep="", collapse="")
+    FTLwtletters<-motif
+    FTLwtmotifs[i,1]<-FTLwtletters
+    # FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+  }
+  
+  if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+    motif<-YYYmotif
+    #add blank spaces if the motif has less than 4 letters to the left/right
+    motif<-c(leftspaces,YYYmotif,rightspaces)
+    #save that motif, which is the Y and +/- 4 amino acids, including truncation
+    motif<-motif[!motif %in% "x"]
+    motif<-paste(motif, sep="", collapse="")
+    FTLwtletters<-motif
+    FTLwtmotifs[i,1]<-FTLwtletters
+    # FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+    
+    
+  }
+  
+}
+
+D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
+D835YAccessionNumbers<-matrix(data = Secondsubbackfreq[1,],ncol = 1)
+
+for (i in 1:nrow(SecondSubstrateSet)){
+  D835letters<-SecondSubstrateSet[i,4:18]
+  D835letters<-D835letters[D835letters !="XXXXX"]
+  D835letters<-paste(D835letters, sep="", collapse="")
+  leftspaces<-c()
+  rightspaces<-c()
+  
+  YYYmotif <- unlist(strsplit(D835letters, split = ""))
+  YYYposition <- match(x = "x", table = YYYmotif)
+  #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+  #just 3 letters to the left of x
+  
+  YYYLettersToTheLeft <- YYYposition - 1
+  #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+  #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+  YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+  #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+  #variable the user puts in is
+  if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+    leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+    rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+    #add blank spaces if the motif has less than 4 letters to the left/right
+    motif<-c(leftspaces,YYYmotif,rightspaces)
+    #save that motif, which is the Y and +/- 4 amino acids, including truncation
+    motif<-motif[!motif %in% "x"]
+    motif<-paste(motif, sep="", collapse="")
+    D835letters<-motif
+    D835Ymotifs[i,1]<-D835letters
+    # D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+  }
+  
+  if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+    motif<-YYYmotif
+    #add blank spaces if the motif has less than 4 letters to the left/right
+    motif<-c(leftspaces,YYYmotif,rightspaces)
+    #save that motif, which is the Y and +/- 4 amino acids, including truncation
+    motif<-motif[!motif %in% "x"]
+    motif<-paste(motif, sep="", collapse="")
+    D835letters<-motif
+    D835Ymotifs[i,1]<-D835letters
+    # D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+  }
+}
+
+
+ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
+ITDAccessionNumbers<-matrix(data = Thirdsubbackfreq[1,],ncol = 1)
+
+for (i in 1:nrow(ThirdSubstrateSet)){
+  ITDletters<-ThirdSubstrateSet[i,4:18]
+  ITDletters<-ITDletters[ITDletters !="XXXXX"]
+  ITDletters<-paste(ITDletters, sep="", collapse="")
+  YYYmotif <- unlist(strsplit(ITDletters, split = ""))
+  leftspaces<-c()
+  rightspaces<-c()
+  YYYposition <- match(x = "x", table = YYYmotif)
+  #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+  #just 3 letters to the left of x
+  
+  YYYLettersToTheLeft <- YYYposition - 1
+  #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+  #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+  YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+  #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+  #variable the user puts in is
+  if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+    leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+    rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+    #add blank spaces if the motif has less than 4 letters to the left/right
+    motif<-c(leftspaces,YYYmotif,rightspaces)
+    #save that motif, which is the Y and +/- 4 amino acids, including truncation
+    motif<-motif[!motif %in% "x"]
+    motif<-paste(motif, sep="", collapse="")
+    ITDletters<-motif
+    ITDmotifs[i,1]<-ITDletters
+    # ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+  }
+  
+  if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+    motif<-YYYmotif
+    #add blank spaces if the motif has less than 4 letters to the left/right
+    motif<-c(leftspaces,YYYmotif,rightspaces)
+    #save that motif, which is the Y and +/- 4 amino acids, including truncation
+    motif<-motif[!motif %in% "x"]
+    motif<-paste(motif, sep="", collapse="")
+    ITDletters<-motif
+    ITDmotifs[i,1]<-ITDletters
+    # ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+  }
+}
+  
+#############################################################################################################################
+#############################################################################################################################
+#############################################################################################################################
+#############################################################################################################################
+#############################################################################################################################
+
+#now look for either commonality or difference.  Actually could you look for both...
+
+if (Are_You_Looking_For_Commonality=="YES"){
+  
+  columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
+  columnalheader<-matrix(columnalheader,nrow = 1)
+
+  SubstrateOverlap1<-intersect(D835Ymotifs,ITDmotifs)
+  SubstrateOverlap1<-as.matrix(SubstrateOverlap1)
+  
+  
+  columnalheader<-c(rep(NA,36))
+  FinalMatrix<-matrix(data =columnalheader,ncol = 1)
+
+  SubstrateOverlapFINAL<-intersect(FTLwtmotifs,SubstrateOverlap1)
+  AccessionOverlap1<-intersect(D835YAccessionNumbers,ITDAccessionNumbers)
+  AccessionOverlapFinal<-intersect(AccessionOverlap1,FTLwtAccessionNumbers)
+  AccessionOverlapFinal<-unlist(AccessionOverlapFinal)
+  
+  for (x in 1:length(AccessionOverlapFinal)) {
+    for (y in 1:ncol(Firstsubbackfreq)) {
+      Acc<-AccessionOverlapFinal[x]
+      SBF<-Firstsubbackfreq[1,y]
+      if(Acc==SBF){
+        FinalMatrix<-cbind(FinalMatrix,Firstsubbackfreq[,y])
+      }
+    }
+  }
+  FinalMatrix<-FinalMatrix[,2:ncol(FinalMatrix)]
+  
+  if(grepl(pattern = "Properties", x=FinalMatrix[22,1])==FALSE){
+    Outputmatrix<-cbind(Firstsubbackfreq[,1],FinalMatrix)
+    write.table(x=Outputmatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
+  } else {
+    write.table(x=FinalMatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
+  }
+  
+  SubstrateMatrix<-SubstrateHeader
+  if(ncol(SubstrateMatrix)>18){
+    SubstrateMatrix<-SubstrateMatrix[,1:18]
+  }
+  
+  for (z in 1:length(SubstrateOverlapFINAL)) {
+    motif<-SubstrateOverlapFINAL[z]
+    newmotif<-unlist(strsplit(motif,split = ""))
+    
+    Addition<-""
+    outputmotif<-c(Addition,Addition,Addition,newmotif)
+    SubstrateMatrix<-rbind(SubstrateMatrix,outputmotif)
+  }
+  write.table(x=SubstrateMatrix,file = Shared_motifs_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
+}

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/C and D finder/commonality-working jan 13 2020.R	Fri Feb 21 16:38:55 2020 -0500
@@ -0,0 +1,285 @@
+FirstSubstrateSet<- read.csv("input1.csv", stringsAsFactors=FALSE, header = FALSE)
+Firstsubbackfreq<- read.csv("input2.csv", header=FALSE, stringsAsFactors=FALSE)
+SubstrateHeader<-FirstSubstrateSet[1,]
+FirstSubstrateSet<- FirstSubstrateSet[2:nrow(FirstSubstrateSet),]
+
+SecondSubstrateSet<- read.csv("input3.csv", stringsAsFactors=FALSE, header = FALSE)
+Secondsubbackfreq<- read.csv("input4.csv", header=FALSE, stringsAsFactors=FALSE)
+SecondSubstrateSet<- SecondSubstrateSet[2:nrow(SecondSubstrateSet),]
+
+
+ThirdSubstrateSet<- read.csv("input5.csv", stringsAsFactors=FALSE, header = FALSE)
+Thirdsubbackfreq<- read.csv("input6.csv", header=FALSE, stringsAsFactors=FALSE)
+ThirdSubstrateSet<- ThirdSubstrateSet[2:nrow(ThirdSubstrateSet),]
+
+
+#ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
+FullMotifsOnly_questionmark<-"NO"
+#If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
+TruncatedMotifsOnly_questionmark<-"NO"
+#if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps)
+Are_You_Looking_For_Commonality<-"YES"
+
+
+#then put the names of your output files here
+Shared_motifs_table<-"sharedmotifs.csv"
+Shared_subbackfreq_table<-"sharedSBF.csv"
+
+# Shared_motifs_table<-"Shared motifs 7-27-17.csv"
+# Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"
+
+First_unshared_motifs_table<-"R1 substrates.csv"
+First_unshared_subbackfreq<-"R1 SBF.csv"
+
+Second_unshared_motifs_table<-"R2 subs.csv"
+Second_unshared_subbackfreq<-"R2 SBf.csv"
+
+Third_unshared_motifs_table<-"R3 subs.csv"
+Third_unshared_subbackfreq<-"R3 SBF.csv"
+
+#final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles.  I think I'll poke around
+#other languages to see if any of them can do it.
+####################################################################################################################################
+
+
+
+
+
+FirstxY<-rep("xY",times=nrow(FirstSubstrateSet))
+FirstSubstrateSet[,11]<-FirstxY
+
+SecondxY<-rep("xY",times=nrow(SecondSubstrateSet))
+SecondSubstrateSet[,11]<-SecondxY
+
+ThirdxY<-rep("xY",times=nrow(ThirdSubstrateSet))
+ThirdSubstrateSet[,11]<-ThirdxY
+
+
+
+
+
+
+
+
+
+
+
+####################################################################################################################################
+####################################################################################################################################
+# better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two 
+# separate proteins thus two separate accession numbers?
+# It should actually output the shared motif and BOTH accession numbers.  Right now it does not, it only maps out the second
+# accession number.  So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number
+####################################################################################################################################
+####################################################################################################################################
+####################################################################################################################################
+####################################################################################################################################
+
+#Create the motif sets, deciding wether or not you're looking for truncated or full here
+#full only
+if (Are_You_Looking_For_Commonality=="YES"){
+
+  
+  ###############################################
+  #ALL motifs, full and truncated
+  
+    FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
+    FTLwtAccessionNumbers=matrix(data = Firstsubbackfreq[1,],ncol=1)
+    
+    for (i in 1:nrow(FirstSubstrateSet)){
+      FTLwtletters<-FirstSubstrateSet[i,4:18]
+      FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
+      FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
+      leftspaces<-c()
+      rightspaces<-c()
+      
+      YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      
+      
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        FTLwtletters<-motif
+        FTLwtmotifs[i,1]<-FTLwtletters
+        # FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        FTLwtletters<-motif
+        FTLwtmotifs[i,1]<-FTLwtletters
+        # FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+        
+        
+      }
+      
+    }
+    
+    D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
+    D835YAccessionNumbers<-matrix(data = Secondsubbackfreq[1,],ncol = 1)
+    
+    for (i in 1:nrow(SecondSubstrateSet)){
+      D835letters<-SecondSubstrateSet[i,4:18]
+      D835letters<-D835letters[D835letters !="XXXXX"]
+      D835letters<-paste(D835letters, sep="", collapse="")
+      leftspaces<-c()
+      rightspaces<-c()
+      
+      YYYmotif <- unlist(strsplit(D835letters, split = ""))
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        D835letters<-motif
+        D835Ymotifs[i,1]<-D835letters
+        D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        D835letters<-motif
+        D835Ymotifs[i,1]<-D835letters
+        D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+    }
+    
+    
+    ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
+    ITDAccessionNumbers<-matrix(data = Thirdsubbackfreq[1,],ncol = 1)
+    
+    for (i in 1:nrow(ThirdSubstrateSet)){
+      ITDletters<-ThirdSubstrateSet[i,4:18]
+      ITDletters<-ITDletters[ITDletters !="XXXXX"]
+      ITDletters<-paste(ITDletters, sep="", collapse="")
+      YYYmotif <- unlist(strsplit(ITDletters, split = ""))
+      leftspaces<-c()
+      rightspaces<-c()
+      YYYposition <- match(x = "x", table = YYYmotif)
+      #position itself tells me how much is to the left of that X by what it's number is.  x at position 4 tells me that there are
+      #just 3 letters to the left of x
+      
+      YYYLettersToTheLeft <- YYYposition - 1
+      #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
+      #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
+      YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
+      #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
+      #variable the user puts in is
+      if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
+        leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
+        rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        ITDletters<-motif
+        ITDmotifs[i,1]<-ITDletters
+        ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+      
+      if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
+        motif<-YYYmotif
+        #add blank spaces if the motif has less than 4 letters to the left/right
+        motif<-c(leftspaces,YYYmotif,rightspaces)
+        #save that motif, which is the Y and +/- 4 amino acids, including truncation
+        motif<-motif[!motif %in% "x"]
+        motif<-paste(motif, sep="", collapse="")
+        ITDletters<-motif
+        ITDmotifs[i,1]<-ITDletters
+        ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
+      }
+    }
+    
+  #############################################################################################################################
+  #############################################################################################################################
+  #############################################################################################################################
+  #############################################################################################################################
+  #############################################################################################################################
+  
+  #now look for either commonality or difference.  Actually could you look for both...
+  
+  if (Are_You_Looking_For_Commonality=="YES"){
+    
+    columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
+    columnalheader<-matrix(columnalheader,nrow = 1)
+
+    SubstrateOverlap1<-intersect(D835Ymotifs,ITDmotifs)
+    SubstrateOverlap1<-as.matrix(SubstrateOverlap1)
+    
+    
+    columnalheader<-c(rep(NA,36))
+    FinalMatrix<-matrix(data =columnalheader,ncol = 1)
+
+    SubstrateOverlapFINAL<-intersect(FTLwtmotifs,SubstrateOverlap1)
+    AccessionOverlap1<-intersect(D835YAccessionNumbers,ITDAccessionNumbers)
+    AccessionOverlapFinal<-intersect(AccessionOverlap1,FTLwtAccessionNumbers)
+    AccessionOverlapFinal<-unlist(AccessionOverlapFinal)
+    
+    for (x in 1:length(AccessionOverlapFinal)) {
+      for (y in 1:ncol(Firstsubbackfreq)) {
+        Acc<-AccessionOverlapFinal[x]
+        SBF<-Firstsubbackfreq[1,y]
+        if(Acc==SBF){
+          FinalMatrix<-cbind(FinalMatrix,Firstsubbackfreq[,y])
+        }
+      }
+    }
+    FinalMatrix<-FinalMatrix[,2:ncol(FinalMatrix)]
+    Outputmatrix<-cbind(Firstsubbackfreq[,1],FinalMatrix)
+    write.table(x=Outputmatrix,file = Shared_subbackfreq_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
+    
+    SubstrateMatrix<-SubstrateHeader
+    if(ncol(SubstrateMatrix)>18){
+      SubstrateMatrix<-SubstrateMatrix[,1:18]
+    }
+    
+    for (z in 1:length(SubstrateOverlapFINAL)) {
+      motif<-SubstrateOverlapFINAL[z]
+      newmotif<-unlist(strsplit(motif,split = ""))
+      
+      Addition<-""
+      outputmotif<-c(Addition,Addition,Addition,newmotif)
+      SubstrateMatrix<-rbind(SubstrateMatrix,outputmotif)
+    }
+    write.table(x=SubstrateMatrix,file = Shared_motifs_table,quote = FALSE,sep = ",",row.names = FALSE,col.names = FALSE,na="")
+  }
+}
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/C and D finder/r1sbf.csv	Fri Feb 21 16:38:55 2020 -0500
@@ -0,0 +1,5343 @@
+Accession Numbers,Amino Acids,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,Properties,Hydrophobic,Polar,Small,Negative,Postive,Amide,Large Aliphatic,Small Aliphatic,Aromatic,Hydroxy,X,Number of Y,Number of pY
+H0YMA0,7.746478873239436,0.7042253521126761,3.5211267605633805,5.633802816901409,3.5211267605633805,7.746478873239436,0.7042253521126761,4.225352112676056,11.971830985915492,10.56338028169014,1.4084507042253522,4.225352112676056,5.633802816901409,4.929577464788732,7.746478873239436,6.338028169014084,3.5211267605633805,7.042253521126761,0.0,2.8169014084507045,,45.77464788732394,38.732394366197184,46.47887323943662,9.15492957746479,20.422535211267604,9.154929577464788,14.788732394366196,22.535211267605632,6.338028169014085,9.859154929577464,,4,1,142
+H0YKK0,5.194805194805195,1.2987012987012987,7.142857142857142,5.194805194805195,3.2467532467532463,3.896103896103896,0.6493506493506493,6.493506493506493,7.142857142857142,18.181818181818183,0.6493506493506493,6.493506493506493,3.896103896103896,3.896103896103896,7.142857142857142,3.2467532467532463,5.194805194805195,7.142857142857142,0.0,3.896103896103896,,50.0,37.66233766233766,43.5064935064935,12.337662337662337,14.935064935064934,10.38961038961039,24.675324675324674,16.233766233766232,7.142857142857142,8.441558441558442,,6,1,154
+P09661,7.0588235294117645,0.7843137254901961,6.666666666666667,7.8431372549019605,2.3529411764705883,7.450980392156863,0.39215686274509803,5.490196078431373,8.235294117647058,13.333333333333334,1.1764705882352942,5.490196078431373,4.705882352941177,3.9215686274509802,7.450980392156863,4.313725490196078,5.490196078431373,5.490196078431373,0.0,2.3529411764705883,,45.49019607843138,40.0,47.450980392156865,14.509803921568627,16.07843137254902,9.411764705882353,18.823529411764707,20.0,4.705882352941177,9.803921568627452,,6,1,255
+Q9NZI8-2,8.904109589041095,0.91324200913242,2.968036529680365,8.21917808219178,2.968036529680365,5.93607305936073,2.054794520547945,7.077625570776255,7.9908675799086755,6.392694063926941,1.82648401826484,4.5662100456621,5.707762557077626,7.534246575342466,5.0228310502283104,6.392694063926941,4.5662100456621,8.21917808219178,0.45662100456621,2.28310502283105,,44.97716894977169,38.35616438356165,48.17351598173516,11.187214611872145,15.068493150684931,12.100456621004565,13.470319634703195,23.059360730593603,5.707762557077625,10.95890410958904,,10,2,438
+Q9NZI8,8.904109589041095,0.91324200913242,2.968036529680365,8.21917808219178,2.968036529680365,5.93607305936073,2.054794520547945,7.077625570776255,7.9908675799086755,6.392694063926941,1.82648401826484,4.5662100456621,5.707762557077626,7.534246575342466,5.0228310502283104,6.392694063926941,4.5662100456621,8.21917808219178,0.45662100456621,2.28310502283105,,44.97716894977169,38.35616438356165,48.17351598173516,11.187214611872145,15.068493150684931,12.100456621004565,13.470319634703195,23.059360730593603,5.707762557077625,10.95890410958904,,10,3,438
+Q9NR09,7.494338068766729,2.2647724933086266,4.982499485278979,5.867819641754169,2.6765493102738316,5.703108914968087,2.964793082149475,4.570722668313774,4.653078031706815,12.806259007617872,2.1618282890673255,3.9118797611694465,5.558987029030265,5.04426600782376,3.7677578752316245,10.06794317479926,6.300185299567635,6.423718344657196,0.9676755198682314,1.8118179946469013,,46.88079061148857,31.192093885114268,52.70743257154623,10.850319127033147,11.385628989087914,8.956145768993206,17.376981675931646,19.621165328392014,5.456042824788964,16.368128474366895,,88,1,4857
+P07384,5.46218487394958,1.5406162464985995,6.582633053221289,7.703081232492997,6.162464985994398,7.142857142857142,1.2605042016806722,4.481792717086835,5.182072829131653,10.224089635854341,2.2408963585434174,3.9215686274509802,3.5014005602240896,3.6414565826330536,7.282913165266107,6.862745098039216,5.042016806722689,6.442577030812324,2.2408963585434174,3.081232492997199,,49.01960784313725,35.57422969187675,46.49859943977591,14.285714285714286,13.725490196078432,7.563025210084033,14.705882352941176,19.047619047619047,11.484593837535014,11.904761904761905,,22,4,714
+P61106,9.767441860465116,1.8604651162790697,4.651162790697675,7.441860465116279,3.7209302325581395,8.372093023255815,1.8604651162790697,6.976744186046512,5.5813953488372094,7.441860465116279,1.8604651162790697,4.651162790697675,3.255813953488372,5.5813953488372094,5.116279069767442,5.5813953488372094,6.511627906976744,4.186046511627907,0.9302325581395349,4.651162790697675,,49.76744186046512,34.883720930232556,48.83720930232558,12.093023255813954,12.558139534883722,10.232558139534884,14.418604651162791,22.325581395348838,9.30232558139535,12.093023255813954,,10,1,215
+X6RFL8,9.94475138121547,1.1049723756906076,4.972375690607735,7.18232044198895,4.41988950276243,7.18232044198895,1.6574585635359116,8.287292817679557,6.077348066298343,7.734806629834254,2.209944751381215,4.972375690607735,1.6574585635359116,4.41988950276243,4.972375690607735,4.972375690607735,7.18232044198895,4.41988950276243,1.1049723756906076,5.524861878453039,,51.93370165745856,34.25414364640884,46.408839779005525,12.154696132596685,12.707182320441989,9.392265193370164,16.02209944751381,21.54696132596685,11.049723756906076,12.154696132596685,,10,1,181
+P54619-2,5.351170568561873,1.0033444816053512,4.682274247491638,6.354515050167224,4.682274247491638,3.3444816053511706,3.3444816053511706,7.357859531772576,7.6923076923076925,11.705685618729097,1.3377926421404682,3.678929765886288,3.678929765886288,2.6755852842809364,4.3478260869565215,7.023411371237458,6.0200668896321075,11.036789297658862,0.6688963210702341,4.013377926421405,,50.501672240802684,32.77591973244147,45.819397993311036,11.036789297658864,15.384615384615385,6.354515050167224,19.063545150501675,19.732441471571903,9.364548494983278,13.043478260869566,,12,1,299
+P54619-3,5.294117647058823,1.1764705882352942,4.411764705882353,7.0588235294117645,4.411764705882353,2.941176470588235,3.2352941176470593,6.764705882352941,6.764705882352941,11.176470588235295,1.4705882352941175,4.117647058823529,4.411764705882353,2.6470588235294117,4.117647058823529,8.529411764705882,6.176470588235294,10.882352941176471,0.5882352941176471,3.823529411764706,,48.52941176470588,32.352941176470594,47.94117647058824,11.470588235294118,14.117647058823529,6.76470588235294,17.941176470588236,19.11764705882353,8.823529411764707,14.705882352941178,,13,1,340
+P54619,5.294117647058823,1.1764705882352942,4.411764705882353,7.0588235294117645,4.411764705882353,2.941176470588235,3.2352941176470593,6.764705882352941,6.764705882352941,11.176470588235295,1.4705882352941175,4.117647058823529,4.411764705882353,2.6470588235294117,4.117647058823529,8.529411764705882,6.176470588235294,10.882352941176471,0.5882352941176471,3.823529411764706,,48.52941176470588,32.352941176470594,47.94117647058824,11.470588235294118,14.117647058823529,6.76470588235294,17.941176470588236,19.11764705882353,8.823529411764707,14.705882352941178,,13,1,340
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